1. DNA: The Chemical Nature of the Gene
Benjamin A. Pierce
GENETICS
A Conceptual Approach
SIXTH EDITION
CHAPTER 10
DNA: The Chemical Nature of the Gene
© 2017 W. H. Freeman and Company

2. Saqqaq people lived in Greenland; DNA sequenced from hair tufts of 4000-year-old male showed the sequences matched those of the Chukchis from Russia.

3. 10.1 Genetic Material Possesses Several Key Characteristics
Genetic material must contain complex information.
Genetic material must replicate faithfully.
Genetic material must encode the phenotype.
Genetic material must have the capacity to vary.

4. 10.2 All Genetic Information Is Encoded in the Structure of DNA or RNA
Early studies of DNA
Figure 10.1
Miescher: nuclein
Kossel: DNA contains four nitrogenous bases
Chargaff’s rules

5. 10.1 Many people have contributed to our understanding of the structure of DNA.

6. 10.2 Johann Friedrich Miescher performed the first chemical analysis of DNA. (a) Portrait of Miescher. (b) Miescher’s laboratory in Tübingen, Germany. [part a: SpL/Science Source. part b: Courtesy of the University of Tübingen Library Image Database, Tübingen, Federal Republic of Germany.]

7. The Search for the Genetic Material
1928 = Frederick Griffith and Streptococcus pneumoniae
1940s = Protein or DNA ??
The case for proteins seemed stronger
1944 = Oswald Avery, Maclyn McCarty and Colin MacLeod working with E.coli and T2
1953 = James Watson and Francis Crick shook the scientific world with their elegant DNA model

8. 10.2 All Genetic Information Is Encoded in the Structure of DNA or RNA
DNA as the source of genetic information
Identification of the transforming principle
Griffith experiment
Figure 10.3
Drs. Avery, Macleod, and McCarty’s experiment
Figure 10.4
The Hershey–Chase experiment
Figure 10.5

9. Frederick Griffith, 1928
Attempting to develop a vaccine against pneumonia
Two strains:
One pathogenic (S strain, capsule)
One non pathogenic (R strain)
S train was killed by heating, and mixed the dead S strain with live R strain
Transformation occurred!!

11. Streptococcus pneumoniae

13. 10.3 Griffith’s experiments demonstrated transformation in bacteria.

14. Observations
Clearly, some chemical component of the dead pathogenic cells caused this heritable change
Griffith called the phenomenon transformation (assimilation of external DNA that causes change in genotype and phenotype)

15. Avery, McCarty and MacLeod 1944
Studied DNA, RNA and protein for 14 years
They worked with Streptococcus pneumoniae
In 1944 Avery, MacLeod and McCarty announced that the transforming agent was DNA
Their discovery was greeted with interest but considerable skepticism

16. Oswald Avery
Colin MacLeod
Maclyn McCarty

18. 10.4 Avery, MacLeod, and McCarty’s experiment revealed the nature of the transforming principle.18

19. Alfred Hershey and Martha Chase, 1952
They worked with bacteriophage (phage) and Escherichia coli (intestines of mammals)
T2 sequesters E. coli’s cell machinery and makes it produce many copies of itself

25. Observations/Conclusions
They where able to observe which type of molecule had entered the bacterial cells and changed them
Phage DNA entered the cell, but the phage protein did not
Conclusion: DNA injected by the phage must be the molecule carrying the genetic information that makes the cells produce new viral DNA and proteins

26. Concept Check 1
If Avery, Macleod, and McCarty had found that samples of heat-killed bacteria treated with RNase and DNase transformed bacteria, but samples treated with protease did not, what conclusion would they have made?
Protease carries out transformation.
RNA and DNA are the genetic materials.
Protein is the genetic material.
RNase and DNase are necessary for transformation.

27. Concept Check 1
If Avery, Macleod, and McCarty had found that samples of heat-killed bacteria treated with RNase and DNase transformed bacteria, but samples treated with protease did not, what conclusion would they have made?
Protease carries out transformation.
RNA and DNA are the genetic materials.
Protein is the genetic material.
RNase and DNase are necessary for transformation.

28. Chargaff It was already know that DNA is a polymer of nucleotides
Analyzed the base composition of DNA from a number of different organisms
He noticed a peculiar regularity in the ratios of nucleotide bases within a single species

29. Erwin Chargaff, 1950

30. Base composition and ratios of bases in DNA from different sources
TABLE 10.1
Base composition and ratios of bases in DNA from different sources
Base Composition (percentage*)
Ratio
Source of DNA A T G C
A/T
G/C
(A + G)/
(T + C)
E. coli
26.0
23.9
24.9
25.2
1.09
0.99
1.04
Yeast
31.3
32.9
18.7
17.1
0.95
1.00
Sea urchin
32.8
32.1
17.7
18.4
1.02
0.96
Rat
28.6
28.4
21.4
21.5
1.01
Human
30.3
19.5
19.9
0.98
*Percentage in moles of nitrogenous constituents per 100 g-atoms of phosphate in hydrolysate corrected for 100% recovery. Source: E. Chargaff and J. Davidson (eds.), The Nucleic Acids, Vol 1 (New York: Academic Press, 1955).

31. Chargaff’s Rules # A approximately equaled the # T
# G approximately equaled the # C
A = 30.3 %
T = 30.3 %
G = 19.5 %
C = 19.9 %
But why was not yet known (structure)

32. 10.2 All Genetic Information Is Encoded in the Structure of DNA or RNA
DNA as the source of genetic information
Watson and Crick’s discovery of the three-dimensional structure of DNA
X-ray diffraction image of DNA
Figure 10.7

33. Building 3-D DNA models (1950s)
Linus Pauling proposed a triple helix model (California Institute of Technology)
Maurice Wilkins and Rosalind Franklin and others (Kings College, London)

34. The story…
James Watson journeyed to Cambridge, where Francis Crick was studying protein structure using X-ray crystallography
Watson visited Maurice Wilkins in the Randall Lab and saw the diffractions images produced by Franklin

35. X-ray Chrystallography
Produces an X-ray diffraction image
The crystal is bombarded with X-rays
The rays are deflected as the pass through the aligned fibers of purified DNA
Mathematical equations are used to translate the patterns into information on the 3D structure of the molecule

36. Figure 10.6 X-ray diffraction provides information about the structures of molecules.

38. Watson and Crick
Built models of a double helix that would conform to the X-ray measurements and to what was known about the chemistry of DNA
They read an unpublished annual report summarizing Franklin’s work where she had concluded that the sugar-phosphate backbones were on the outside of the double helix

39. pyrimidine
purine
pyrimidine
purine

41. Great idea!!!
The arrangement was appealing because it put the relatively hydrophobic nitrogenous bases towards the interior
Sugar-phosphate backbones are antiparallel
Nitrogenous bases are paired in specific combinations (maintain uniform diameter)

43. April 1953
Watson and Crick surprised the scientific world with a succinct, one-page paper in Nature
The beauty of the model is that is suggested a mechanism for replication

44. 1962: Nobel Prize awarded Watson and Crick Also to Maurice Wilkins
But not given to Rosalind Franklin!
She sadly died of cancer in 1958

45. Base Paring to a Template Strand
Watson and Crick wrote a second paper in which they stated their hypothesis for how DNA replicates

46. The semiconservative model remained untested for several years
Other models were:
Conservative model
Dispersive model

47. 10.2 All Genetic Information Is Encoded in the Structure of DNA or RNA
RNA as genetic information:
In most organisms, DNA carries genetic information; in some, RNA carries genetic information instead.
Tobacco mosaic virus (Fig. 10.9)

48. 10.9 Fraenkel-Conrat and Singer’s experiment demonstrated that RNA in the tobacco mosaic virus carries the genetic information.

49. The primary structure of DNA:
10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix
The primary structure of DNA:
Deoxyribonucleotides
Nucleotides
Three parts: sugar, a phosphate, and a base
Nucleotide structure: Figure 10.10
Purine or pyrimidine base: Figure `

50. 10.10 A nucleotide contains either a ribose sugar (in RNA) or a deoxyribose sugar (in DNA). The carbon atoms of the sugars are assigned primed numbers.

51. 10. 11 A nucleotide contains either a purine or a pyrimidine base
10.11 A nucleotide contains either a purine or a pyrimidine base. The atoms of the rings in the bases are assigned unprimed numbers.

52. 10.12 A nucleotide contains a phosphate group.

53. 10. 13 There are four types of DNA nucleotides
10.13 There are four types of DNA nucleotides. These nucleotides are deoxyribonucleoside 5′-monophosphates.

54. Names of DNA bases, nucleotides, and nucleosides
TABLE 10.2
Names of DNA bases, nucleotides, and nucleosides
Adenine
Guanine
Thymine
Cytosine
Base symbol A G T C
Nucleotide
Deoxyadenosine 5' monophosphate
Deoxyguanosine 5' monophosphate
Deoxythymidine 5' monophosphate
Deoxycytidine 5' monophosphate
Nucleotide symbol
dAMP
dGMP
dTMP
dCMP
Nucleoside
Deoxyadenosine
Deoxyguanosine
Deoxythymidine
Deoxycytidine
Nucleoside symbol dA dG dT dC

55. Secondary structure of DNA:
10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix
Secondary structure of DNA:
The double helix
Backbone formed through phosphodiester bonds
Hydrogen bond and base pairing
Antiparallel complementary DNA strands
Figure 10.14

56. 10.14 DNA and RNA consist of polynucleotide strands.

57. Concept Check 3 The antiparallel nature of DNA refers to
its charged phosphate groups.
the pairing of bases on one strand with bases on the other strand.
the formation of hydrogen bonds between bases from opposite strands.
the opposite direction of the two strands of nucleotides.

58. Concept Check 3 The antiparallel nature of DNA refers to
its charged phosphate groups.
the pairing of bases on one strand with bases on the other strand.
the formation of hydrogen bonds between bases from opposite strands.
the opposite direction of the two strands of nucleotides.

59. Secondary structure of DNA:
10.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form
a Double Helix
Secondary structure of DNA:
Three-dimensional structure identified by Watson and Crick refers to B-DNA
Figure 10.15
Different secondary structures
Figure 10.16

60. 10.15 B-DNA consists of a right-handed helix with approximately 10 bases per turn. (a) Space-filling model of B-DNA showing major and minor grooves. (b) Diagrammatic representation.

61. 10. 16 DNA can assume several different secondary structures. [After J
10.16 DNA can assume several different secondary structures. [After J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 6th ed. (New York: W. H. Freeman and Company, 2002), pp. 785 and 787.]

62. 10.17 Pathways of information transfer within the cell.

63. 10.4 Special Structure Can Form in DNA and RNA
Hairpin structure: In single strands of nucleotides, when sequences of nucleotides on the same strand are inverted complements, a hairpin structure will be formed.
Figure (a)
When the complementary sequences are contiguous, the hairpin has a stem but no loop.
Figure (b)
RNA molecules may contain numerous hairpins, allowing them to fold up into complex structures.
Figure (c)

64. Figure 10.17 (a) A DNA secondary structure - hairpin

65. Figure 10.17 (b) A DNA secondary structure - stem

66. Figure 10. 17 (c) Secondary structure of RNA component of RNase P of E
Figure (c) Secondary structure of RNA component of RNase P of E. coli.

67. 10.4 Special Structure Can Form in DNA and RNA
H-DNA: three-stranded (triplex); formed when DNA unwinds and one strand pairs with double-stranded DNA from another part of the molecule
Often occurs in long sequences of only purines or only pyrimidines
Common in mammalian genomes

69. 10.4 Special Structure Can Form in DNA and RNA
DNA methylation
Methyl groups added to nucleotide bases
Related to gene expression in eukaryotes
Affects the three-dimensional structure of DNA

70. 10.20 In eukaryotic DNA, cytosine bases are often methylated to form 5-methylcytosine.